X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fvamsas%2Fobjects%2Fsimple%2FAlignment.java;h=574a1e9a261c20c1b28f665ab8f40bcdeac0dafb;hb=b08ae4419c138647b696f440e09a75a39e63383e;hp=7328cbd8a6c452538dd8c975b39bde8d26b8ce61;hpb=357598ffdf5c04f08a2a370218f0e22551ee9231;p=jalview.git

diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 7328cbd..574a1e9 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -3,175 +3,166 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
-package vamsas.objects.simple;
-
-public class Alignment  extends vamsas.objects.simple.Object  implements java.io.Serializable {
-    private java.lang.String gapchar;
-    private java.lang.String[] method;
-    private vamsas.objects.simple.SequenceSet seqs;
-    private vamsas.objects.simple.Sequence[] seqsAsArray;
-
-    public Alignment() {
-    }
-
-    public Alignment(
-           java.lang.String gapchar,
-           java.lang.String[] method,
-           vamsas.objects.simple.SequenceSet seqs,
-           vamsas.objects.simple.Sequence[] seqsAsArray) {
-           this.gapchar = gapchar;
-           this.method = method;
-           this.seqs = seqs;
-           this.seqsAsArray = seqsAsArray;
-    }
-
-
+ */
+
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+package vamsas.objects.simple;
+
+public class Alignment extends vamsas.objects.simple.Object
+    implements java.io.Serializable {
+    private java.lang.String gapchar;
+    private java.lang.String[] method;
+    private vamsas.objects.simple.SequenceSet seqs;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public Alignment() {
+    }
+
+    public Alignment(java.lang.String gapchar, java.lang.String[] method,
+        vamsas.objects.simple.SequenceSet seqs) {
+        this.gapchar = gapchar;
+        this.method = method;
+        this.seqs = seqs;
+    }
+
     /**
-     * Gets the gapchar value for this Alignment.
-     * 
-     * @return gapchar
-     */
-    public java.lang.String getGapchar() {
-        return gapchar;
-    }
-
-
-    /**
-     * Sets the gapchar value for this Alignment.
-     * 
-     * @param gapchar
-     */
-    public void setGapchar(java.lang.String gapchar) {
-        this.gapchar = gapchar;
-    }
-
-
-    /**
-     * Gets the method value for this Alignment.
-     * 
-     * @return method
-     */
-    public java.lang.String[] getMethod() {
-        return method;
-    }
-
-
+ * Gets the gapchar value for this Alignment.
+ *
+ * @return gapchar
+ */
+    public java.lang.String getGapchar() {
+        return gapchar;
+    }
+
     /**
-     * Sets the method value for this Alignment.
-     * 
-     * @param method
-     */
-    public void setMethod(java.lang.String[] method) {
-        this.method = method;
-    }
-
-
+ * Sets the gapchar value for this Alignment.
+ *
+ * @param gapchar
+ */
+    public void setGapchar(java.lang.String gapchar) {
+        this.gapchar = gapchar;
+    }
+
     /**
-     * Gets the seqs value for this Alignment.
-     * 
-     * @return seqs
-     */
-    public vamsas.objects.simple.SequenceSet getSeqs() {
-        return seqs;
-    }
-
-
+ * Gets the method value for this Alignment.
+ *
+ * @return method
+ */
+    public java.lang.String[] getMethod() {
+        return method;
+    }
+
     /**
-     * Sets the seqs value for this Alignment.
-     * 
-     * @param seqs
-     */
-    public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
-        this.seqs = seqs;
-    }
-
-
+ * Sets the method value for this Alignment.
+ *
+ * @param method
+ */
+    public void setMethod(java.lang.String[] method) {
+        this.method = method;
+    }
+
     /**
-     * Gets the seqsAsArray value for this Alignment.
-     * 
-     * @return seqsAsArray
-     */
-    public vamsas.objects.simple.Sequence[] getSeqsAsArray() {
-        return seqsAsArray;
-    }
-
-
+ * Gets the seqs value for this Alignment.
+ *
+ * @return seqs
+ */
+    public vamsas.objects.simple.SequenceSet getSeqs() {
+        return seqs;
+    }
+
     /**
-     * Sets the seqsAsArray value for this Alignment.
-     * 
-     * @param seqsAsArray
-     */
-    public void setSeqsAsArray(vamsas.objects.simple.Sequence[] seqsAsArray) {
-        this.seqsAsArray = seqsAsArray;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Alignment)) return false;
-        Alignment other = (Alignment) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = super.equals(obj) && 
-            ((this.gapchar==null && other.getGapchar()==null) || 
-             (this.gapchar!=null &&
-              this.gapchar.equals(other.getGapchar()))) &&
-            ((this.method==null && other.getMethod()==null) || 
-             (this.method!=null &&
-              java.util.Arrays.equals(this.method, other.getMethod()))) &&
-            ((this.seqs==null && other.getSeqs()==null) || 
-             (this.seqs!=null &&
-              this.seqs.equals(other.getSeqs()))) &&
-            ((this.seqsAsArray==null && other.getSeqsAsArray()==null) || 
-             (this.seqsAsArray!=null &&
-              java.util.Arrays.equals(this.seqsAsArray, other.getSeqsAsArray())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = super.hashCode();
-        if (getGapchar() != null) {
-            _hashCode += getGapchar().hashCode();
-        }
-        if (getMethod() != null) {
-            for (int i=0;
-                 i<java.lang.reflect.Array.getLength(getMethod());
-                 i++) {
-                java.lang.Object obj = java.lang.reflect.Array.get(getMethod(), i);
-                if (obj != null &&
-                    !obj.getClass().isArray()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
-        }
-        if (getSeqs() != null) {
-            _hashCode += getSeqs().hashCode();
-        }
-        if (getSeqsAsArray() != null) {
-            for (int i=0;
-                 i<java.lang.reflect.Array.getLength(getSeqsAsArray());
-                 i++) {
-                java.lang.Object obj = java.lang.reflect.Array.get(getSeqsAsArray(), i);
-                if (obj != null &&
-                    !obj.getClass().isArray()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-}
+ * Sets the seqs value for this Alignment.
+ *
+ * @param seqs
+ */
+    public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
+        this.seqs = seqs;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Alignment)) {
+            return false;
+        }
+
+        Alignment other = (Alignment) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = super.equals(obj) &&
+            (((this.gapchar == null) && (other.getGapchar() == null)) ||
+            ((this.gapchar != null) && this.gapchar.equals(other.getGapchar()))) &&
+            (((this.method == null) && (other.getMethod() == null)) ||
+            ((this.method != null) &&
+            java.util.Arrays.equals(this.method, other.getMethod()))) &&
+            (((this.seqs == null) && (other.getSeqs() == null)) ||
+            ((this.seqs != null) && this.seqs.equals(other.getSeqs())));
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = super.hashCode();
+
+        if (getGapchar() != null) {
+            _hashCode += getGapchar().hashCode();
+        }
+
+        if (getMethod() != null) {
+            for (int i = 0; i < java.lang.reflect.Array.getLength(getMethod());
+                    i++) {
+                java.lang.Object obj = java.lang.reflect.Array.get(getMethod(),
+                        i);
+
+                if ((obj != null) && !obj.getClass().isArray()) {
+                    _hashCode += obj.hashCode();
+                }
+            }
+        }
+
+        if (getSeqs() != null) {
+            _hashCode += getSeqs().hashCode();
+        }
+
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+}